10-115753077-T-G

Variant names:

• chr10-115753077-T-G
• rs10490919
• NM_207303.4:c.3903+25722T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_207303.4(ATRNL1):​c.3903+25722T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.468 in 151,804 control chromosomes in the GnomAD database, including 18,344 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.47 (18344 hom., cov: 31)
• Consequence: ATRNL1 NM_207303.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.331
• Publications: 12 publications found

Genes affected

ATRNL1 (HGNC:29063): (attractin like 1) Predicted to enable carbohydrate binding activity. Predicted to be involved in several processes, including animal organ morphogenesis; cell migration; and substrate adhesion-dependent cell spreading. Predicted to act upstream of or within G protein-coupled receptor signaling pathway. Predicted to be located in membrane. Predicted to be integral component of membrane. Predicted to be active in basement membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.731 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_207303.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATRNL1	NM_207303.4	MANE Select	c.3903+25722T>G		intron	N/A	NP_997186.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATRNL1	ENST00000355044.8	TSL:1 MANE Select	c.3903+25722T>G		intron	N/A	ENSP00000347152.3
	ATRNL1	ENST00000650603.1		n.3795+25722T>G		intron	N/A	ENSP00000497485.1

Frequencies

GnomAD3 genomes AF: 0.468 AC: 71057 AN: 151686 Hom.: 18338 Cov.: 31

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.534

Gnomad AMR AF: 0.599

Gnomad ASJ AF: 0.602

Gnomad EAS AF: 0.751

Gnomad SAS AF: 0.468

Gnomad FIN AF: 0.535

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.534

Gnomad OTH AF: 0.508

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.468 AC: 71077 AN: 151804 Hom.: 18344 Cov.: 31 AF XY: 0.473 AC XY: 35104 AN XY: 74170

African (AFR) AF: 0.245 AC: 10167 AN: 41434

American (AMR) AF: 0.599 AC: 9114 AN: 15206

Ashkenazi Jewish (ASJ) AF: 0.602 AC: 2081 AN: 3458

East Asian (EAS) AF: 0.750 AC: 3872 AN: 5160

South Asian (SAS) AF: 0.470 AC: 2263 AN: 4816

European-Finnish (FIN) AF: 0.535 AC: 5644 AN: 10544

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.533 AC: 36207 AN: 67870

Other (OTH) AF: 0.511 AC: 1079 AN: 2112

Alfa AF: 0.509 Hom.: 14653

Bravo AF: 0.466

Asia WGS AF: 0.584 AC: 2033 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.7
DANN	Benign	0.66
PhyloP100		0.33
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10490919; hg19: chr10-117512588;